Aligments for a candidate for acs in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for acs in Pseudomonas simiae WCS417

Align 4-hydroxybutyrate-CoA ligase (EC 6.2.1.40) (characterized)
to candidate GFF2136 PS417_10895 AMP-dependent synthetase

Query= BRENDA::A4YDT1
         (564 letters)



>lcl|FitnessBrowser__WCS417:GFF2136 PS417_10895 AMP-dependent
           synthetase
          Length = 566

 Score =  373 bits (957), Expect = e-107
 Identities = 223/544 (40%), Positives = 300/544 (55%), Gaps = 36/544 (6%)

Query: 35  LRRFNWVRDVFEDIHVKERGSKTALIWRDINTGEEAKLSYHELSLMSNRVLSTLRKHGLK 94
           L  FNW  D F+ +     G+    +W     G E + S+ +L+  SN+V + LR  G+ 
Sbjct: 31  LGEFNWALDYFDAM---AEGNPADALWIVEEDGSEQRYSFQQLAARSNQVANHLRALGVN 87

Query: 95  KGDVVYLMTKVHPMHWAVFLAVIKGGFVMVPSATNLTVAEMKYRFSDLKPSAIISDSLRA 154
           +GD V LM       W   LA  K G V++P+   L   +++ R              R 
Sbjct: 88  RGDRVLLMLGNDVALWDTMLAAFKLGAVVIPATALLNPDDLRDRIE------------RG 135

Query: 155 SVMEEALGSLKVEKFL----------IDGKRETWNSLEDESSNAEPEDTRGE----DVII 200
            V    +G   V KF           +      W +        E  + +G     D ++
Sbjct: 136 QVRHVVVGEAHVHKFAGLAQGCSRICVGSAPAGWVAHNAAFEYPEQFEAQGRTLATDPML 195

Query: 201 NYFTSGTTGMPKRVIHTAVSYPVGSITTASIVGVRESDLHLNLSATGWAKFAWSSFFSPL 260
            YFTSGTT  PK V+H+  SYPVG ++T   +G++  DLHLN+S+ GWAK AWS  F+P 
Sbjct: 196 LYFTSGTTSKPKMVLHSHQSYPVGHLSTMYWIGLQPGDLHLNISSPGWAKHAWSCLFAPW 255

Query: 261 LVGATVVGINYEGKLDTRRYLGEVENLGVTSFCAPPTAWRQFITLDLDQFRFE-RLRSVV 319
             GA +  I+   +      L  +E  GVTS CAPPT WR  I  DL  +R    LR +V
Sbjct: 256 NAGACIF-IHNVARFSAPALLSALERYGVTSLCAPPTVWRMLIQEDLASYRPRLSLRELV 314

Query: 320 SAGEPLNPEVIKIWKDKFNLTIRDFYGQTETTAMVGNFPFLKVKPGSMGKPHPLYDIRLL 379
            AGEPLNPE+I+  +  + L +RD +GQ+ETTA+VGN P   +KPGSMG+P P Y + LL
Sbjct: 315 GAGEPLNPEIIEQIQQAWGLPLRDGFGQSETTALVGNTPGQLLKPGSMGRPLPGYQVALL 374

Query: 380 DDEGKEITKPYEVGHITVKLNPRPIGLFLGYSDE-KKNMESFREGYYYTGDKAYFDEEGY 438
           D +G     P   G + + L+ RP+GL L Y D  +K  E  R+GYY TGD A  D +GY
Sbjct: 375 DPDGI----PGNEGEVALPLDVRPLGLMLCYEDSPEKTAEVMRDGYYRTGDTAQIDADGY 430

Query: 439 FYFVGRGDDVIKTSDYRVGPFEVESALLEHPAVAEAAVVGVPDTVRWQLVKAYIVLKKGY 498
             FVGR DDV K SDYR+ PFE+ESAL+EHPAV E AVV  PD +R  + KA+++L    
Sbjct: 431 ITFVGRADDVFKASDYRISPFELESALIEHPAVMEVAVVPSPDPLRLAVPKAFLILAHDE 490

Query: 499 MPSKELAEEIREKMKTLLSPYKVPRIIEFVDELPKTISGKIRRVELRKREEEKRKKGEVG 558
             S  LA+ I    +  L+PYK  R IEFV ELPKTISGKIRRVELR+ E  +R+    G
Sbjct: 491 PGSAALAQHILAFAREHLAPYKRVRRIEFVTELPKTISGKIRRVELRQMEVLRRQGDTRG 550

Query: 559 QNEY 562
           ++E+
Sbjct: 551 EHEH 554


Lambda     K      H
   0.318    0.137    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 747
Number of extensions: 35
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 564
Length of database: 566
Length adjustment: 36
Effective length of query: 528
Effective length of database: 530
Effective search space:   279840
Effective search space used:   279840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources